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E46 (1999 - 2006) The fourth generation 3 Series (E46 chassis) was introduced in 1999 and set the standard for engineering and performance during it's years of production including being named to Car & Driver's 10 best list every one of those years! ! -- View the E46 Wiki

So I have a 2005 325i with a M56 engine 117k miles and I have occasionally over the last month been having misfires on Cylinder 6 at start up with a rough idle for about 30 seconds then it feels fine, and the rpms instead of reving up past 1000 rpms and dropping back down to the 750 range will on start up slowing increase to 1000 rpm, hold there for the 30 seconds then slowy drop to 750 and then the SES light comes on telling me ihave the misfire (error code 306).
I've replaced the spark plugs and boots just about 3 mo ago along with the vanos seals and camshaft position sensors and cleaned the ICV. Trying to diagnose what else it might be thats causing this.

I've replaced the spark plugs and boots just about 3 mo ago along with the vanos seals and camshaft position sensors and cleaned the ICV. Trying to diagnose what else it might be thats causing this.

You were on the right track but stopped short of a likely cause. The COIL itself is probably bad on #6. Swap it with #5 and see if the new code it throws is p0305, in other words, see if the code follows the coil. Very common.

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I had a similiar problem at about 65K miles. Cylinder 3 was misfiring. Tried swapping the coil, new plugs, clean the MAF sensor, even a new o2 sensor for that bank, plenty of fuel injection cleaner. Nothing solved the problem. One dealer wanted to run a battery of tests which I though was ridiculous and expensive. Other dealer said it was the fuel injector for that cylinder, which rarely fails but he felt that was my problem. Sure enough, they tested the fuel injector, it was bad, replaced it and all problems solved. Cost was $575 at dealer.

Sorry i abandoned this for so long. So I took it to the dealer 3 months back since the misfires would come and then disappear and I couldn't solve it. The went through the steps and at swapping spark plugs the misfire stayed at 6, then they did the boots and suddenly 4 out 6 were misfiring. So since the boot were under warranty they just replaced all six and the misfire went away and they called it good. Starting 1 month ago random misfires and rough idle started coming back again. So I'll be taking it back since the spark plug and any sensors are covered under the sulev warranty and seeing what they say.